my last few prints have these steps in them. not sure if it is slic3r or my stl's. i can run the gcode in a simulator and also shows the steps....so it is not the printer.

I just got into 3d scanning and cant seem to get a good gcode file from one. but no issues from cadd created objects

my process:
-3d scan via Skanect save as 50-80mb .stl
-open in netfabb basic and clean up and save 18-30mb .stl (still has random faces in the middle of the object)
-open in slic3r and save a 1-7mb .gcode
-print

have meshlab, but haven't found a good use for it yet.

running x64 versions of slic3r
1.0.0RC1 - crashes
0.9.10b - print steps and would occasionally use 7,3gb of mem and lock up
0.9.9 - x86 - print steps

stl is too large to upload
AMG STL

Was slic3r the only slicer you tried? I use slic3r 99% of the time, but every once in a while I come across something that it can't slice properly. This is when I use skeinforge.

I would recommend that you try either skeinforge, or kisslicer and see what you get.